my 60+ mph vibration was fixed by balancing the tires, good thing i have access to a balancer at my school lol. also remember to fill the tires to 32psi b4 balancing.

 

I had this problem with my 94 es300. Once I got new tires and had the car aligned, the vibrating went away and never came back.

 

the thump might be the sparkplugs? I bought the car around march of this year and i havent changed the sparkplugs and dont know when they were changed last. I get the thump going into seconds gear and a little thump in third, thought it was motor mounts but isnt. It could be spark plugs?